Using Golden Gate Assembly to Test Bacterial Promoter Hypotheses

1. Using Golden Gate Assembly to Test Bacterial Promoter Hypotheses GCAT Synthetic Biology Workshop 2014

2. GGA with Annealed Oligos BsaI BsaI Destination plasmid GFP RFP + Sticky End Sticky End Annealed oligos Product GFP RFP

3. Anneal Oligos • Mix oligos with annealing buffer and dH20 1 ul 100 uM Top strand oligo 1 ul 100 uM Bottom strand oligo 2 ul 10X oligoannealing buffer (1 M NaCl, 100 mMTris) 16 ul dH20 • Boil 4 minutes in beaker with ~400 ml H2O • Turn off heat and let cool > 2 hours

4. Oligo Concentration • Calculate concentration (ng/ul) of oligos • Annealing reduced concentration from 100 uM to 5 uM • Example uses 40 bpoligos 670 ug/umol-bpx 40 bpx 5 umol/L x 10-6L/ul = 0.13 ug/ul = 130 ng/ul

5. Dilution of Oligos • GGA will use 20 ng of Receiving plasmide J100091, which is ~3000 bp • Calculate annealed oligoamount 20 ng plasmid x (40 bpoligos/3000 bp plasmid) = 0.27 ngoligos • Dilution of oligos (130 ng/ul) / (0.27 ng/ul) = 481 Add 1 ul of Annealed oligos to 480 ul dH2O

6. Golden Gate Assembly Reaction 20 cycles 37° C for 1 minute 16° C for 1 minute 37° C for 15 minutes

7. Transformation of Competent Cells • Thaw one tube JM109 Competent Cells (50 ul) • Add 50 ul dilution buffer for each transformation (up to 8 transformations/tube) • Add 50 ul diluted cells to GGA reaction tube • Mix gently and incubate on ice 5 min. • Plate onto LB + Amp

8. What is the consensus sequence for the two elements of a bacterial promoter? -10 element = t80a95t45a60a50t96 Optimal position is -10, but position varies from -18 to -9 from center of -10 element to TSS at +1 Subscripts indicate percentage of time the base is present -35 element = t82T84G78A65C54A45 Position varies, but spacing between -35 and -10 elements is 16-18 bp in 90% of known promoters Optimal spacing is 17 bp Subscripts indicate percentage of time the base is present Source: Genes IX, 2008, by Benjamin Lewin

9. Transcription Initiation • RNAP binds to DNA and engages in direct exchange of one sequence for another • Affinity of RNAP for nonspecific DNA decreased by Sigma factor • RNAP + Sigma “touches down” at -35 element • Contact is extended to -10 element, covering ~77 bp in “closed” binary complex • Melting is facillitated by A+T content of -10 element - of ~12 bp from -10 element to +1 produces “open” binary complex • Incorporation of NTPs forms ternary complex, and multiple rounds of abortive initiation occur • Change in RNAP structure occurs, Sigma factor is released or changes form, and it covers ~50 bp • RNAP clears the promoter, shortens to cover only 30-40 bp, and elongation occurs at a rate of ~40 nt/sec

10. pTac Promoter • Hybrid promoter constructed from pTrp and pLac promoters in E. coli • Efficiency of promotion measure to be 2-3 times great than pTrp and 7-11 times greater than pLac • Perfect matches to -1- and -35 consensus sequences and 16 bp between them -35 -10 +1 DeBoer HA, Comstock LJ, Vasser M (1982) PNAS 80, 21-25.

11. Mutation #3

12. Mutation #4

13. Mutation #5

14. Mutation F

15. Vector Only

16. Mutation #3

17. Mutation #4

18. Mutation #5

19. Mutation F